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haplo.stats (version 1.7.9)

Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Description

Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.

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Version

Install

install.packages('haplo.stats')

Monthly Downloads

1,909

Version

1.7.9

License

GPL (>= 2)

Maintainer

Jason Sinnwell

Last Published

April 11th, 2018

Functions in haplo.stats (1.7.9)

geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes
get.hapPair

Get a list of objects for haplotype pairs
hapPower.demo

Set of haplotypes and frequencies for power and sample size calculations
haplo.hash

Integer Rank Codes for Haplotypes
haplo.scan

Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window
haplo.em.fitter

Compute engine for haplotype EM algorithm
summary.haplo.glm

Print and summary of a haplo.glm object
anova.haplo.glm

Analysis of variance for haplo.glm model fit
Ginv

Compute Generalized Inverse of Input Matrix
haplo.glm

GLM Regression of Trait on Ambiguous Haplotypes
haplo.model.frame

Sets up a model frame for haplo.glm
haplo.score.merge

Merge haplo.score And haplo.group Objects
haplo.score

Score Statistics for Association of Traits with Haplotypes
haplo.score.slide

Score Statistics for Association of Traits with Haplotypes
print.haplo.em

Print contents of a haplo.em object
find.haplo.beta.qt

Find beta coefficients for risk haplotypes, for specified r2
print.haplo.scan

Print a haplo.scan object
print.haplo.group

Print a haplo.group object
fitted.haplo.glm

Fitted values from haplo.glm fit
chisq.power

Power and sample size for the chi-square distribution
printBanner

Print a nice banner
haplo.design

Build a design matrix for haplotypes
haplo.cc

Haplotype Association Analysis in a Case-Control design
f.power

Power and sample size for the F distribution
haplo.group

Frequencies for Haplotypes by Grouping Variable
haplo.glm.control

Create list of control parameters for haplo.glm
print.haplo.score

Print a haplo.score object
residuals.haplo.glm

Accessing residuals for haplo.glm fit
dglm.fit

Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
hla.demo

HLA Loci and Serologic Response to Measles Vaccination
locator.haplo

Find Location from Mouse Clicks and Print Haplotypes on Plot
setupGeno

Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
locus

Creates an object of class "locus"
plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics
seqhap.dat

Simulated data for seqhap examples
louis.info

Louis Information for haplo.glm
plot.haplo.score.slide

Plot a haplo.score.slide Object
score.sim.control

Create the list of control parameters for simulations in haplo.score
x.sexcheck

consistency checks for x.linked locus
na.geno.keep

Remove rows with NA in covariates, but keep genotypes with NAs
seqhap

Sequential Haplotype Scan Association Analysis for Case-Control Data
print.haplo.score.merge

Print a haplo.score.merge object
print.haplo.score.slide

Print the contents of a haplo.score.slide object
summaryGeno

Summarize Full Haplotype Enumeration on Genotype Matrix
vcov.haplo.glm

variance-covariance matrix of a fitted haplo.glm object
plot.seqhap

Plot a seqhap object
print.haplo.cc

Print a haplo.cc object
summary.haplo.em

Summarize contents of a haplo.em object
geno1to2

convert genotype matrix from 1-column 2-column
haplo.em

EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em.control

Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.power.qt

Compute either power or sample size for haplotype associations with a quantitative trait.
haplo.power.cc

Compute either power or sample size for haplotype associations in a case-control study.